update to pybind11 v2.2.0

python/py_basictypes.cpp

@@ -16,9 +16,9 @@ namespace py = pybind11;
 using namespace catana;
 
 
-PYBIND11_PLUGIN(basictypes)
+PYBIND11_MODULE(basictypes, m)
 {
-    py::module m("basictypes", "python bindings of basic types used in CatAna");
+    m.doc() = "python bindings of basic types used in CatAna";
 
     // Binding for the "Point" class, with cartesian and spherical output methods
     py::class_<Point>(m, "Point", py::buffer_protocol(), R"pbdoc(
@@ -125,11 +125,11 @@ Create a PointContainer from a (numpy) array containing the coordinates
                 // Buffer definition, so that we can call numpy.array(point_container) in python
         .def_buffer([](PointContainer& oc) -> py::buffer_info {
             return py::buffer_info(
-                    (double*) oc.data(),
+                    &(oc.data()->r),
                     sizeof(double),
                     py::format_descriptor<double>::format(),
                     2,
-                    { oc.size(), 3},
+                    std::array<long int, 2>{static_cast<long int>(oc.size()), 3},
                     { sizeof(double) * 3, sizeof(double)}
             );
         })
@@ -215,6 +215,4 @@ Evaluate the FunctionInterpolator at the given values x.
 Parameters:
     x (numpy.ndarray[float]): evaluation points
         )pbdoc", py::arg("x"));
-
-    return m.ptr();
 }

python/py_besseltools.cpp

@@ -9,8 +9,8 @@ namespace py = pybind11;
 using namespace catana;
 
 
-PYBIND11_PLUGIN(besseltools) {
-    py::module m("besseltools", "python binding to besseltools library (part of CatAna)");
+PYBIND11_MODULE(besseltools, m) {
+    m.doc() = "python binding to besseltools library (part of CatAna)";
 
     py::class_<besseltools::SphericalBesselZeros>(m, "SphericalBesselZeros", R"pbdoc(
             A root generator for spherical Bessel functions.
@@ -82,6 +82,4 @@ Computes :math:`\int_0^{r_{max}} \; w(r) \; j_l(k_1 r) \; j_l(k_2 r) \;\; dr`
     k2 (float): frequency of other spherical Bessel function
         )pbdoc", py::arg("w"), py::arg("l"), py::arg("r_max"), py::arg("k1"), py::arg("k2")
     );
-
-    return m.ptr();
 }

python/py_decomposition.cpp

@@ -10,8 +10,8 @@
 namespace py = pybind11;
 using namespace catana;
 
-PYBIND11_PLUGIN(decomposition) {
-  py::module m("decomposition", "python binding for SFB decomposition of particle positions (part of CatAna)");
+PYBIND11_MODULE(decomposition, m) {
+  m.doc() = "python binding for SFB decomposition of particle positions (part of CatAna)";
 
   // Initialization of random numbers. Once with given seed, once random seed
   m.def("init_random", py::overload_cast<unsigned int>(&init_random), R"pbdoc(
@@ -151,6 +151,4 @@ This method makes use of the fast pixelized decomposition scheme.
         f_lm(k) components
 )pbdoc", py::arg("pixelized_point_container"), py::arg("lmax"), py::arg("nmax"), py::arg("rmax"),
         py::arg("store_flmn") = false, py::arg("verbose") = true);
-
-  return m.ptr();
 }

python/py_io.cpp

@@ -16,8 +16,8 @@ using record_sd = io::SphericalRecord<double>;
 using record_sd_3dex = io::SphericalRecord<double, io::SphericalTextFormat::THREEDEX>;
 
 
-PYBIND11_PLUGIN(io) {
-  py::module m("io", "python binding for in/output of particle positions (part of CatAna)");
+PYBIND11_MODULE(io, m) {
+  m.doc() = "python binding for in/output of particle positions (part of CatAna)";
 
   // Initialization of random numbers. Once with given seed, once random seed
   m.def("init_random", py::overload_cast<unsigned int> (&init_random), R"pbdoc(
@@ -343,8 +343,8 @@ Constructor from a HEALPix map array
               sink (Sink): to where the filtered points are stored
               buffer_size (int): size of the buffer (in number of points). Faster if larger, but consumes more memroy.
               verbose (bool): if ``True``, print additional logging information to stdout
-      )pbdoc", py::arg("source"), py::arg("sink"), py::arg("buffer_size")=1000000, py::arg("verbose")=true,
-      py::keep_alive<1, 2>(), py::keep_alive<1, 3>())
+      )pbdoc", py::arg("source"), py::arg("sink"), py::arg("buffer_size")=1000000, py::arg("verbose")=true)
+//      py::keep_alive<1, 2>(), py::keep_alive<1, 3>())  TODO: add keep_alive back in (removed because of SIGSEGV)
       .def("add_filter", &io::FilterStream::add_filter, R"pbdoc(
           Add a Filter to the pipeline.
 
@@ -361,7 +361,7 @@ Constructor from a HEALPix map array
 
           Parameters:
               source (Source): a source instance
-      )pbdoc", py::arg("source"), py::keep_alive<1, 2>())
+      )pbdoc") //, py::arg("source"), py::keep_alive<1, 2>())  // TODO: add keep_alive back in
       .def("run", &io::FilterStream::run, R"pbdoc(
           Run the pipeline
 
@@ -402,6 +402,4 @@ Constructor from a HEALPix map array
           Returns:
               int: number of points written to the sink
       )pbdoc", py::arg("temp_filename")="tmp.bin", py::arg("subsample_size")=0, py::arg("remove_temp")=true);
-
-  return m.ptr();
 };

test/python/io_test.py

@@ -3,10 +3,12 @@
 import pytest
 import os
 
+
 @pytest.fixture
 def datadir():
     return os.path.join(os.path.dirname(__file__), '..', 'test_data')
 
+
 class TestText(object):
     def test_source(self, datadir):
         s = catana.io.CartesianTextSource(os.path.join(datadir, "mock_data.txt"))